When you are in combat with more than one monster, you cannot resolve ANY aspect of the combat until ALL monsters are defeated or until the munchkins flee. This means that if you use an ability to make one monster disappear, you cannot claim levels and/or Treasures for beating it (depending on the method used) unless you can then kill or defeat all the remaining monsters. You cannot, for instance, use your Wizard to charm one monster and take its Treasures before fighting the rest. Combat isn't over until the WHOLE combat is over.
One thing to remember is that if a monster has a special ability, it applies to the entire combat. A monster that is immune to fire/flame attacks, for instance, means that no fire/flame attacks give a bonus at all, even if other monsters don't share that vulnerability.